7YXA

XFEL crystal structure of the human sphingosine 1 phosphate receptor 5 in complex with ONO-5430608

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B	Sphingosine 1-phosphate receptor 5,Soluble cytochrome b562	polymer	458	49922.6	2	UniProt (Q9H228) UniProt (P0ABE7) Pfam (PF00001) Pfam (PF07361) In PDB	Homo sapiens (human)	S1P receptor 5,S1P5,Endothelial differentiation G-protein-coupled receptor 8,Sphingosine 1-phosphate receptor Edg-8,S1P receptor Edg-8,Cytochrome b-562
2	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	2	Chemie (NAG)
3	A, B	4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid	non-polymer		404.5	2	Chemie (B2O)
4	A	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	non-polymer		356.5	3	Chemie (OLC)
5	B	OLEIC ACID	non-polymer		282.5	2	Chemie (OLA)
6		water	water		18.0	194	Chemie (HOH)

Sequence modifications

A, B: 1 - 223 (UniProt: Q9H228)

PDB	External Database	Details
Met -26	-	initiating methionine
Lys -25	-	expression tag
Thr -24	-	expression tag
Ile -23	-	expression tag
Ile -22	-	expression tag
Ala -21	-	expression tag
Leu -20	-	expression tag
Ser -19	-	expression tag
Tyr -18	-	expression tag
Ile -17	-	expression tag
Phe -16	-	expression tag
Cys -15	-	expression tag
Leu -14	-	expression tag
Val -13	-	expression tag
Phe -12	-	expression tag
Ala -11	-	expression tag
Asp -10	-	expression tag
Tyr -9	-	expression tag
Lys -8	-	expression tag
Asp -7	-	expression tag
Asp -6	-	expression tag
Asp -5	-	expression tag
Asp -4	-	expression tag
Ala -3	-	linker
Gly -2	-	linker
Arg -1	-	linker
Ala 0	-	linker

A, B: 1001 - 1106 (UniProt: P0ABE7)

PDB	External Database	Details
Trp 1007	Met 29	engineered mutation
Ile 1102	His 124	engineered mutation
Leu 1106	Arg 128	engineered mutation

A, B: 241 - 321 (UniProt: Q9H228)

PDB	External Database	Details
Gly 322	-	linker
Arg 323	-	linker
Pro 324	-	linker
Leu 325	-	expression tag
Glu 326	-	expression tag
Val 327	-	expression tag
Leu 328	-	expression tag
Phe 329	-	expression tag
Gln 330	-	expression tag
Gly 331	-	expression tag
Pro 332	-	expression tag
His 333	-	expression tag
His 334	-	expression tag
His 335	-	expression tag
His 336	-	expression tag
His 337	-	expression tag
His 338	-	expression tag
His 339	-	expression tag
His 340	-	expression tag
His 341	-	expression tag
His 342	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	2
	Total formula weight	99845.2
Non-Polymers*	Number of molecules	9
	Total formula weight	2886.0
All*	Total formula weight	102731.2

*Water molecules are not included.